Ok, great! I just wanted to make sure I wasn't doing something stupid! :) I'll file the BugZilla issue now (and download the source so that I can hopefully provide a patch).
On Thu, Jul 3, 2008 at 11:17 AM, Richard Holland <[EMAIL PROTECTED]> wrote: > Apparently not. I don't think they're part of the formal Genbank > specification, or at least not the one that was current at the time > the parser was written (in 2004). If they were, then we must have > missed them out by accident. Sorry! Could you raise a bug report via > BugZilla onthe BioJava website and someone will look into it as soon > as they get a chance. > > cheers, > Richard > > 2008/7/3 James Carman <[EMAIL PROTECTED]>: >> I'm trying to parse the file: >> >> ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_mammalian/vertebrate_mammalian12.protein.gpff.gz >> >> using: >> >> RichSequence.IOTools.readGenbankProtein() >> >> and I keep getting this error (the date column is from my build server >> which runs this "loader", sorry): >> >> [10:51:36]: org.biojava.bio.BioException: Could not read sequence >> [10:51:36]: at >> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113) >> [10:51:36]: at >> com.pg.iip.loader.pubrec.RefSeqLoader.loadPublicRecords(RefSeqLoader.java:106) >> [10:51:36]: at >> com.pg.iip.loader.pubrec.PublicRecordLoader.doLoad(PublicRecordLoader.java:248) >> [10:51:36]: at >> com.pg.iip.loader.AbstractLoader.execute(AbstractLoader.java:56) >> [10:51:36]: at >> com.pg.iip.loader.LoaderUtils.executeLoader(LoaderUtils.java:20) >> [10:51:36]: at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) >> [10:51:36]: at >> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) >> [10:51:36]: at >> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) >> [10:51:36]: at java.lang.reflect.Method.invoke(Method.java:585) >> [10:51:36]: at >> com.pg.iip.loader.plugin.RunLoaderMojo.invoke(RunLoaderMojo.java:95) >> [10:51:36]: at >> com.pg.iip.loader.plugin.RunLoaderMojo.execute(RunLoaderMojo.java:142) >> [10:51:36]: at >> org.apache.maven.plugin.DefaultPluginManager.executeMojo(DefaultPluginManager.java:447) >> [10:51:36]: at >> org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoals(DefaultLifecycleExecutor.java:539) >> [10:51:36]: at >> org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeStandaloneGoal(DefaultLifecycleExecutor.java:493) >> [10:51:36]: at >> org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoal(DefaultLifecycleExecutor.java:463) >> [10:51:36]: at >> org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoalAndHandleFailures(DefaultLifecycleExecutor.java:311) >> [10:51:36]: at >> org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeTaskSegments(DefaultLifecycleExecutor.java:278) >> [10:51:36]: at >> org.apache.maven.lifecycle.DefaultLifecycleExecutor.execute(DefaultLifecycleExecutor.java:143) >> [10:51:36]: at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:333) >> [10:51:36]: at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:126) >> [10:51:36]: at org.apache.maven.cli.MavenCli.main(MavenCli.java:282) >> [10:51:36]: at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) >> [10:51:36]: at >> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) >> [10:51:36]: at >> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) >> [10:51:36]: at java.lang.reflect.Method.invoke(Method.java:585) >> [10:51:36]: at >> org.codehaus.classworlds.Launcher.launchEnhanced(Launcher.java:315) >> [10:51:36]: at org.codehaus.classworlds.Launcher.launch(Launcher.java:255) >> [10:51:36]: at >> org.codehaus.classworlds.Launcher.mainWithExitCode(Launcher.java:430) >> [10:51:36]: at org.codehaus.classworlds.Launcher.main(Launcher.java:375) >> [10:51:36]: Caused by: org.biojava.bio.seq.io.ParseException: Could >> not understand position: bond(39,96 >> [10:51:36]: at >> org.biojavax.bio.seq.io.GenbankLocationParser.parsePosition(GenbankLocationParser.java:285) >> [10:51:36]: at >> org.biojavax.bio.seq.io.GenbankLocationParser.parseLocString(GenbankLocationParser.java:271) >> [10:51:36]: at >> org.biojavax.bio.seq.io.GenbankLocationParser.parseLocation(GenbankLocationParser.java:131) >> [10:51:36]: at >> org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:490) >> [10:51:36]: at >> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) >> [10:51:36]: ... 28 more >> >> Does the parser not understand "Bond" features? >> _______________________________________________ >> Biojava-l mailing list - [email protected] >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
